RegulonDB RegulonDB 10.8: Operon Form
   

yceD-rpmF-plsX-fabHDG-acpP-fabF operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yceD-rpmF-plsX-fabHDG-acpP-fabF
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: yceD-rpmF
Gene(s): yceD, rpmF   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR represses yceD gene expression under anaerobiosis, but it is not known which of the two promoters transcribing the gene is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Tanaka Y., et al., 1989
Promoter
Name: yceDp1
+1: 1146649
Distance from start of the gene: 145
Sequence:
Note(s): This promoter appears to have more transcriptional sites at positions 1146648/49/50 , as determined by high-throughput screening of maps of promoters Lacoux C,2020.
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Salgado H, et al., 2012
[1] Tanaka Y., et al., 1989


Transcription unit       
Name: yceD-rpmF
Gene(s): yceD, rpmF   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR represses yceD gene expression under anaerobiosis, but it is not known which of the two promoters transcribing the gene is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Tanaka Y., et al., 1989
Promoter
Name: yceDp2
+1: 1146791
Distance from start of the gene: 3
Sequence:
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Salgado H, et al., 2012
[1] Tanaka Y., et al., 1989


Transcription unit       
Name: rpmF-plsX-fabHDG
Gene(s): rpmF, plsX, fabH, fabD, fabG   Genome Browser M3D Gene expression COLOMBOS
Note(s): The rpmF and pslX-fab genes are cotranscribed, and this is the fist example where lipid biosynthetic genes and a ribosomal protein gene comprise an operon Podkovyrov S,1995
It is probable that yceD-rpmF-plsX-fabHDG-acpP-fabF cluster genes are regulated together, since they are involved in the same functional class. However, a transcript that continues through the entire gene cluster has not been determined by Northern blotting or by experiments with polar mutations.
Evidence: [PM] Polar mutation
Reference(s): [3] Podkovyrov S., et al., 1995
Promoter
Name: rpmFp
+1: 1147338
Distance from start of the gene: 29
Sequence: acccatttgccgtattagccagcttaaagcgtaagtaattggtgctccccgttggatcggGgataaaccgtaattgaggag
Evidence: [HTIM]
Reference(s): [4] Mendoza-Vargas A., et al., 2009


Transcription unit       
Name: plsX-fabHDG
Gene(s): plsX, fabH, fabD, fabG   Genome Browser M3D Gene expression COLOMBOS
Note(s): The pslX transcripts were detected only by RT-PCR, and therefore the lengths of these transcripts are unknown. They could initiate at the promoters located upstream of g30k as determined by Tanaka Y,1989and/or at the fabH promoter mapped by Podkovyrov SM,1996CITS:[9642179]|.
It is probable that yceD-rpmF-plsX-fabHDG-acpP-fabF cluster genes are regulated together, since they are involved in the same functional class. However, a transcript that continues through the entire gene cluster has not been determined by Northern blotting nor by experiments with polar mutations.
Evidence: [PM] Polar mutation
Reference(s): [5] Zhang Y., et al., 1998
Promoter
Name: plsXp
+1: 1147577
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 44
Sequence: ggccgcaaggtcatcgctaagtaatcacgcatctgcgtgatgaagcttagtgaggattttCcccaggcaactggggaaaga
                        -35                     -10         +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [6] Thomason MK., et al., 2015


Transcription unit          
Name: fabHDG
Gene(s): fabH, fabD, fabG   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is part of a group of genes (encoding acyl carrier protein and several key fatty acid biosynthetic enzymes) which are not transcribed as a classic operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene.
The fabHGD operon is subject to stringent control Podkovyrov SM,1996
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [7] Podkovyrov SM., et al., 1996
Promoter
Name: fabHp
+1: 1148516
Distance from start of the gene: 243
Sequence:
Note(s): fabHp is subject to stringent control, and it is responsible for ~40% of all transcripts for fabH Podkovyrov SM,1996
fabH has a GC-rich motif discriminator sequence between the -10 region and the start site, which is a characteristic feature of the stringently regulated promoter Podkovyrov SM,1996
The fabH promoter is not only a contributor to its expression under all conditions, but also other activators might compensate to activate fabH expression when FadR is absent, and/or with basal expression of the fabHGD genes My L,2013
Evidence: [TIM]
Reference(s): [7] Podkovyrov SM., et al., 1996
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FadR activator fabHp 1148470 1148486 -38.0 attcagtcacCTCAACCCCGACCAGTAtaacggcgcc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [8], [9]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition fabHp ppGpp and its cofactor, DksA, inhibit in two ways the transcription of fabHp: 1) they directly inhibit its transcription, and 2) they inhibit fadR expression, which is an activator of the fabHDG operon My L,2013 [GEA] [8]
[7]
Evidence: [GEA] Gene expression analysis
Reference(s): [8] My L., et al., 2013
[7] Podkovyrov SM., et al., 1996


Transcription unit       
Name: acpP
Gene(s): acpP   Genome Browser M3D Gene expression COLOMBOS
Note(s): acpP expression is not under growth rate control Zhang Y,1996.
A consensus sequence resembling the FadR-binding site was identified at position -40 upstream from the acpP promoter Henry MF,1992. However, analysis in a gel shift assay of the acpP fragment containing the putative FadR-binding site compared to the purified FadR protein gave no significant shift of the DNA band, nor was there a significant change in acpP expression in a fadR null mutant strain. These findings indicate that FadR is not involved in the regulation of ACP expression Zhang Y,1996.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [10] Rawlings M., et al., 1992
[11] Zhang Y., et al., 1996
Promoter
Name: acpPp
+1: 1151575
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 40
Sequence: atcgtggtaagacctgccgggatttagttgcaaatttttcaacattttatacactacgaaAaccatcgcgaaagcgagttt
Note(s): acpPp is the major transcription start site for the acpP-fabF operon; however, there is a minor signal for this 1 nt downstream of the acpPp promoter Zhang Y,1996.
Evidence: [HIPP]
[TIM]
Reference(s): [11] Zhang Y., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: aagtgaacatCTCCAGGCGGTCGTTCGACCGCCTGAGTtttatctttt
Reference(s): [10] Rawlings M., et al., 1992


Transcription unit       
Name: acpP-fabF
Gene(s): acpP, fabF   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is part of a group of genes (encoding acyl carrier protein and several key fatty acid biosynthetic enzymes) which are not transcribed as a classic operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene Zhang Y,1996.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [11] Zhang Y., et al., 1996
Promoter
Name: acpPp
+1: 1151575
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 40
Sequence: atcgtggtaagacctgccgggatttagttgcaaatttttcaacattttatacactacgaaAaccatcgcgaaagcgagttt
Note(s): acpPp is the major transcription start site for the acpP-fabF operon; however, there is a minor signal for this 1 nt downstream of the acpPp promoter Zhang Y,1996.
Evidence: [HIPP]
[TIM]
Reference(s): [11] Zhang Y., et al., 1996


Transcription unit       
Name: fabG-acpP
Gene(s): fabG, acpP   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is part of a group of genes (encoding acyl carrier protein and several key fatty acid biosynthetic enzymes) which are not transcribed as a classic operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [10] Rawlings M., et al., 1992
[11] Zhang Y., et al., 1996


Transcription unit       
Name: fabF
Gene(s): fabF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [11] Zhang Y., et al., 1996


Transcription unit       
Name: fabDG-acpP
Gene(s): fabD, fabG, acpP   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is part of a group of genes (encoding acyl carrier protein and several key fatty acid biosynthetic enzymes) which are not transcribed as a classic operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [11] Zhang Y., et al., 1996


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.3 1151860 1151900 agtgaacatcTCCAGGCGGTCGTTCGACCGCCTGAGTTTTATCTTTTTGTcccactagaa
  terminator -11.6 1151568 1151601 ttttatacacTACGAAAACCATCGCGAAAGCGAGTTTTGATAGgaaatttaag
  anti-terminator -12.3 1151834 1151874 gattacatcaACGGCCACCAGGCGTAAGTGAACATCTCCAGGCGGTCGTTcgaccgcctg
  anti-anti-terminator -10.5 1151809 1151848 aatcaccaccGTTCAGGCTGCCATTGATTACATCAACGGCCACCAGGCGtaagtgaaca
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"




Reference(s)    

 [1] Tanaka Y., Tsujimura A., Fujita N., Isono S., Isono K., 1989, Cloning and analysis of an Escherichia coli operon containing the rpmF gene for ribosomal protein L32 and the gene for a 30-kilodalton protein., J Bacteriol 171(10):5707-12

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [3] Podkovyrov S., Larson TJ., 1995, Lipid biosynthetic genes and a ribosomal protein gene are cotranscribed., FEBS Lett 368(3):429-31

 [4] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [5] Zhang Y., Cronan JE., 1998, Transcriptional analysis of essential genes of the Escherichia coli fatty acid biosynthesis gene cluster by functional replacement with the analogous Salmonella typhimurium gene cluster., J Bacteriol 180(13):3295-303

 [6] Thomason MK., Bischler T., Eisenbart SK., Forstner KU., Zhang A., Herbig A., Nieselt K., Sharma CM., Storz G., 2015, Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli., J Bacteriol 197(1):18-28

 [7] Podkovyrov SM., Larson TJ., 1996, Identification of promoter and stringent regulation of transcription of the fabH, fabD and fabG genes encoding fatty acid biosynthetic enzymes of Escherichia coli., Nucleic Acids Res 24(9):1747-52

 [8] My L., Rekoske B., Lemke JJ., Viala JP., Gourse RL., Bouveret E., 2013, Transcription of the Escherichia coli Fatty Acid Synthesis Operon fabHDG Is Directly Activated by FadR and Inhibited by ppGpp., J Bacteriol 195(16):3784-95

 [9] Zhang F., Ouellet M., Batth TS., Adams PD., Petzold CJ., Mukhopadhyay A., Keasling JD., 2012, Enhancing fatty acid production by the expression of the regulatory transcription factor FadR., Metab Eng 14(6):653-60

 [10] Rawlings M., Cronan JE., 1992, The gene encoding Escherichia coli acyl carrier protein lies within a cluster of fatty acid biosynthetic genes., J Biol Chem 267(9):5751-4

 [11] Zhang Y., Cronan JE., 1996, Polar allele duplication for transcriptional analysis of consecutive essential genes: application to a cluster of Escherichia coli fatty acid biosynthetic genes., J Bacteriol 178(12):3614-20


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